Fix (=really add) Clinker #12472
Fix (=really add) Clinker #12472
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Update to build as recipe not appearing in bioconda packages
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The build log shows "nothing to be done". This still won't build anything. |
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Still "nothing to be done". Do not merge. |
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Thanks for looking at this @epruesse I'm still unclear what is going on with this recipe. Can you advise on what is preventing this recipe from appearing in bioconda, i.e not available from conda or here https://bioconda.github.io/recipes.html, but appears in the master branch. |
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@andrewlonsdale I had this 'nothing to be done' issue, I think it was caused by naming the file meta.yml instead of meta.yaml. |
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Aaaah! Thanks @tfursten - that seems to be the case here too. |
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You probably have something in the recipe that gets stuck. Your job timed out after 5 hours of processing. |
Recipe now passes local circlei build, mulled-tests and linting, so🤞
Recipe fails locally with build of 2
| - samtools | ||
| - star ==2.5.3a | ||
| - bioconductor-biomart ==2.34.2 | ||
| - bioconductor-gviz ==1.22.3 |
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If you need to pin that tightly, you should distribute an environment file. Please make these something like
- star >=2.5.3a, <3
- bioconductor-biomart >=2.34.2, <3
- bioconductor-gviz >=1.22.3, <2
| sha256: "5dbb97da27f29f53a8282e456ba0093bbdde292eb9e76405434117da4d1a76be" | ||
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| build: | ||
| number: 1 |
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Should be 0 - no packages exist yet.
| @@ -0,0 +1,44 @@ | |||
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| @@ -15,8 +15,6 @@ END | |||
| ) | |||
| # Clinker wrapper - invoke bpipe | |||
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| #bpipe -p option1="something" -p option2="something_else" [...] $CLINKERDIR/workflow/clinker.pipe /path/to/*.fastq.gz | |||
| # parse and accept parameters in bpipe style, then pass on to fixed clinker.pipe location | |||
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It appears this entire file should be distributed upstream. Can you create a PR there and link it in the recipe?
| notes: | | ||
| Wrapper script provided to indicate clinker is a bpipe pipeline, | ||
| provide example command from wiki, and also a passthrough option. | ||
| Tests run from /tmp to avoid Docker permission error. |
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Would you like to add yourself as recipe-maintainers: [username]?
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This can be closed, #25647 is latest update to recipe and fixes other issues |
These are minor changes intended to trigger the build process again as previous addition of this recipe passed tests and was merged into master (#10244) but the recipe does not appear to be available.